Project summary It is now clear that hybridization between species is much more common than previously recognized. As a result, we are now realizing that the genomes of many modern species, including our own, are a patchwork of regions derived from past hybridization events. Despite this increasing appreciation of the ubiquity of hybridization, we still understand very little about the impact of hybridization on adaptation and genome evolution. Addressing these topics is the major focus of research in the lab. An outstanding question is where in the genome hybrid ancestry persists and what processes shape this distribution. Recent work, including my own, has demonstrated that regions of the genome with higher densities of genes and conserved elements are less likely to move between species. While this general pattern has been well-established, identifying the individual loci under selection after hybridization and the mechanisms of selection acting on these loci remains a major challenge. The proposed work will leverage dense time-series sampling of hybrid populations of swordtail fish, a model system for studying hybridization, to develop new approaches to address these questions. Although in most cases there is strong selection against hybridization between divergent species, sometimes hybridization can allow adaptive alleles to move between species. Known examples of such ?adaptive introgression? include the spread of resistance to rodent poisons and to insecticides in malarial mosquitoes. One shortcoming of current methods for detecting such events is that they ignore the prevalence of negative selection against hybridization, which can obscure signals. We propose to develop new methods for identifying selection and adaptive introgression after hybridization that perform well in this context. This work will yield new insights into the role of hybridization in adaptation and trait evolution. In addition, hybridization can have global impacts on genome evolution. Since hybridization combines two divergent genomes, this can also mean combining two different recombination landscapes (since in some cases recombination hotspots evolve quickly between species). Indeed, recombination divergence has been implicated in hybrid sterility in some species. We will use modeling to explore how recombination landscapes are expected to evolve after hybridization in species with different mechanisms for specifying recombination hotspots, and compare this to empirical data we will generate. Together, this work will give unprecedented insight into how hybridization impacts the evolution of the genome, from selection on individual loci to the structure of the genome. !